Surface capping not working

[yazan.abbas@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-51-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-06-25)
Description
surface cap doesnt work. tried multiple offset valies but that didnt help.

Log:
UCSF ChimeraX version: 0.91 (2019-06-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open maps_and_models/State1_composite.cif name State1

Summary of feedback from opening maps_and_models/State1_composite.cif  
---  
warnings | skipping chem_comp category: Missing column 'type' near line 297  
Unknown polymer entity '?' near line 342  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
skipping chem_comp category: Missing column 'type' near line 72840  
skipping chem_comp category: Missing column 'type' near line 72867  
  
Chain information for State1 #1  
---  
Chain | Description  
A1 A2 A3 | No description available  
B1 | No description available  
B2 | No description available  
B3 | No description available  
C | No description available  
D | No description available  
E1 E2 E3 | No description available  
F | No description available  
G1 | No description available  
G2 | No description available  
G3 | No description available  
K1 | No description available  
K2 | No description available  
K3 | No description available  
a | No description available  
ac | No description available  
b | No description available  
c1 c2 c3 c4 c5 c6 c7 c8 c9 | No description available  
d | No description available  
e | No description available  
f | No description available  
pr | No description available  
  

> open maps_and_models/J1509_state1_Vo.mrc

Opened J1509_state1_Vo.mrc, grid size 340,340,340, pixel 1.06, shown at level
0.16, step 2, values float32  

> set bgColor white

> set silhouettes true

> camera ortho

> surface cap true

> lighting soft shadows true intensity 0.1

> close #1.1

> split #1 chains

Chain information for State1 A1 #1.1  
---  
Chain | Description  
A1 | No description available  
  
Chain information for State1 A2 #1.2  
---  
Chain | Description  
A2 | No description available  
  
Chain information for State1 A3 #1.3  
---  
Chain | Description  
A3 | No description available  
  
Chain information for State1 B1 #1.4  
---  
Chain | Description  
B1 | No description available  
  
Chain information for State1 B2 #1.5  
---  
Chain | Description  
B2 | No description available  
  
Chain information for State1 B3 #1.6  
---  
Chain | Description  
B3 | No description available  
  
Chain information for State1 C #1.7  
---  
Chain | Description  
C | No description available  
  
Chain information for State1 D #1.8  
---  
Chain | Description  
D | No description available  
  
Chain information for State1 E1 #1.9  
---  
Chain | Description  
E1 | No description available  
  
Chain information for State1 E2 #1.10  
---  
Chain | Description  
E2 | No description available  
  
Chain information for State1 E3 #1.11  
---  
Chain | Description  
E3 | No description available  
  
Chain information for State1 F #1.12  
---  
Chain | Description  
F | No description available  
  
Chain information for State1 G1 #1.13  
---  
Chain | Description  
G1 | No description available  
  
Chain information for State1 G2 #1.14  
---  
Chain | Description  
G2 | No description available  
  
Chain information for State1 G3 #1.15  
---  
Chain | Description  
G3 | No description available  
  
Chain information for State1 K1 #1.16  
---  
Chain | Description  
K1 | No description available  
  
Chain information for State1 K2 #1.17  
---  
Chain | Description  
K2 | No description available  
  
Chain information for State1 K3 #1.18  
---  
Chain | Description  
K3 | No description available  
  
Chain information for State1 a #1.19  
---  
Chain | Description  
a | No description available  
  
Chain information for State1 ac #1.20  
---  
Chain | Description  
ac | No description available  
  
Chain information for State1 b #1.21  
---  
Chain | Description  
b | No description available  
  
Chain information for State1 c1 #1.22  
---  
Chain | Description  
c1 | No description available  
  
Chain information for State1 c2 #1.23  
---  
Chain | Description  
c2 | No description available  
  
Chain information for State1 c3 #1.24  
---  
Chain | Description  
c3 | No description available  
  
Chain information for State1 c4 #1.25  
---  
Chain | Description  
c4 | No description available  
  
Chain information for State1 c5 #1.26  
---  
Chain | Description  
c5 | No description available  
  
Chain information for State1 c6 #1.27  
---  
Chain | Description  
c6 | No description available  
  
Chain information for State1 c7 #1.28  
---  
Chain | Description  
c7 | No description available  
  
Chain information for State1 c8 #1.29  
---  
Chain | Description  
c8 | No description available  
  
Chain information for State1 c9 #1.30  
---  
Chain | Description  
c9 | No description available  
  
Chain information for State1 d #1.31  
---  
Chain | Description  
d | No description available  
  
Chain information for State1 e #1.32  
---  
Chain | Description  
e | No description available  
  
Chain information for State1 f #1.33  
---  
Chain | Description  
f | No description available  
  
Chain information for State1 pr #1.34  
---  
Chain | Description  
pr | No description available  
  
Split State1 (#1) into 34 models  

> dssp

> select #1.1-3

13993 atoms, 14279 bonds, 3 models selected  

> name frozen subunitA sel

> select #1.4-6

10847 atoms, 11060 bonds, 3 models selected  

> name frozen subunitB sel

> select #1.7

2927 atoms, 2981 bonds, 1 model selected  

> name frozen subunitC sel

> select #1.8

1726 atoms, 1744 bonds, 1 model selected  

> name frozen subunitD sel

> select #1.9-11

5040 atoms, 5079 bonds, 3 models selected  

> name frozen subunitE sel

> select #1.12

876 atoms, 890 bonds, 1 model selected  

> name frozen subunitF sel

> select #1.13-15

2392 atoms, 2401 bonds, 3 models selected  

> name frozen subunitG sel

> select #1.16-18

5441 atoms, 5542 bonds, 3 models selected  

> name frozen SidK sel

> select #1.19

5615 atoms, 5754 bonds, 1 model selected  

> name frozen V0a sel

> select #1.21

1503 atoms, 1537 bonds, 1 model selected  

> name frozen V0b sel

> select #1.22-30

9612 atoms, 9747 bonds, 9 models selected  

> name frozen V0cring sel

> select #1.31

2833 atoms, 2899 bonds, 1 model selected  

> name frozen V0d sel

> select #1.32

628 atoms, 653 bonds, 1 model selected  

> name frozen V0e sel

> select #1.33

675 atoms, 691 bonds, 1 model selected  

> name frozen V0RNAseK sel

> select #1.20

337 atoms, 347 bonds, 1 model selected  

> name frozen V0Ac45 sel

> select #1.34

443 atoms, 456 bonds, 1 model selected  

> name frozen V0PRR sel

> hide SidK target c

> hide subunitG target c

> hide subunitF target c

> hide subunitE target c

> hide subunitC target c

> hide subunitA target c

> hide subunitB target c

> hide subunitD target c

> hide subunitF target c

> color subunitA #F2EA42 target cabp

> color subunitB #D01F26 target cabp

> color subunitC #996633 target cabp

> color subunitD #3A53A3 target cabp

> color subunitE #804F9F target cabp

> color subunitF #B9529E target cabp

> color subunitG #fce94f target cabp

> color SidK #D2D2D2 target cabp

> color V0a #8ae234 target cabp

> color V0b #9d42bf target cabp

> color V0cring #e182d9 target cabp

> color V0d #8ab7ff target cabp

> color V0e #3465a4 target cabp

> color V0RNAseK #cc0000 target cabp

> color V0Ac45 #EEEEEC target cabp

> color V0PRR #edd400 target cabp

> select clear

> hide atoms

> show cartoons

> surface dust #2 size 6

> volume #2 step 1 level 0.5 color #EEEEEC surfaceSmoothing true
subdivideSurface true smoothingIterations 4

> cartoon style V0cring modeHelix tube

> hide SidK target c

> hide subunitG target c

> hide subunitF target c

> hide subunitE target c

> hide subunitC target c

> hide subunitA target c

> hide subunitB target c

> hide subunitD target c

> hide subunitF target c

> color V0Ac45 #eeeeec target c

> ui mousemode rightMode pivot

> toolshed show "Volume Viewer"

> toolshed show "Model Panel"

> cartoon style V0b modeHelix tube

> show #!2 models

> color zone #2 near #1 distance 3 sharpEdges true

> ui mousemode rightMode rotate

> ui mousemode rightMode pivot

> volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true
subdivideSurface true smoothingIterations 4

> volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true
subdivideSurface true smoothingIterations 4

Expected a keyword  

Expected a keyword  

> color zone #2 near #1 distance 3 sharpEdges true update false

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/std_commands/color.py", line 1248, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,
auto_update = update)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 14, in color_zone  
zc.set_vertex_colors()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 84, in set_vertex_colors  
replace = True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 123, in color_zone_sharp_edges  
ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 147, in _edge_cuts  
f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
ValueError: Cut fraction -0.27227 is out of range (0,1)  
  
ValueError: Cut fraction -0.27227 is out of range (0,1)  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
  
See log for complete Python traceback.  
  

> volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true
subdivideSurface true smoothingIterations 4

> color zone #2 near #1 distance 3 sharpEdges true update false

> color zone #2 near #1 distance 2.5 sharpEdges true update false

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/std_commands/color.py", line 1248, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,
auto_update = update)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 14, in color_zone  
zc.set_vertex_colors()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 84, in set_vertex_colors  
replace = True)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 123, in color_zone_sharp_edges  
ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 147, in _edge_cuts  
f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, distance)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
ValueError: Cut fraction 1.7919 is out of range (0,1)  
  
ValueError: Cut fraction 1.7919 is out of range (0,1)  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/surface/colorzone.py", line 181, in _edge_cut_position  
raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)  
  
See log for complete Python traceback.  
  

> volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true
subdivideSurface true smoothingIterations 4

> volume #2 step 1 level 0.501 color #eeeeec surfaceSmoothing true
subdivideSurface true smoothingIterations 4

> color zone #2 near #1 distance 3 sharpEdges true update false

> save after_colorzone.png

> volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true
subdivideSurface true smoothingIterations 4

> save before_colorzone.png

> surface cap

Clip caps on, offset 0.01  

> surface cap offset 1

> surface cap offset 0.1

> lighting soft

> lighting full

> lighting flat

> lighting soft

> lighting soft

> lighting soft

> volume selMaps style surface

> volume selMaps style mesh

> volume selMaps style surface

> surface cap

Clip caps on, offset 0.1  

Missing "offset" keyword's argument  

Expected true or false or a keyword  

> surface cap false

> surface cap true

> surface cap

Clip caps on, offset 0.1  

> surface cap offset 10

> surface cap offset 1

> surface cap offset -1

> ui mousemode rightMode translate

> ui mousemode rightMode zoom

> surface cap offset -1

> surface cap offset -20




OpenGL version: 3.3.0 NVIDIA 418.56
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Surface caps do not display on volume surfaces that have been colored with "sharpEdges true" because the sharp edges option makes the triangle geometry of the surface disconnected at the edges. This causes the computation of the intersection of the clip plane with the surface not to see closed loops where it places caps.

The color zone option "sharpEdges true" obviously has lots of problems. We should probably document those as a first step. There are ways to fix them but it is complex enough that it may be not be soon.

[yazan.abbas@…]

Hi Tom,

Thanks for your reply. That doesn't seem to the be the problem. I tried
again in a new session and a recently loaded map and submitted another bug
report for that.

Yazan

On Wed, Jun 26, 2019 at 6:52 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

Duplicate of #2130. Problem was "surface dust" caused caps not to display if parts of surface were hidden. Surface caps still will not display if "sharpEdges true" is used.